{"action":"created","issue":{"url":"https://api.github.com/repos/isetbio/isetbio/issues/232","repository_url":"https://api.github.com/repos/isetbio/isetbio","labels_url":"https://api.github.com/repos/isetbio/isetbio/issues/232/labels{/name}","comments_url":"https://api.github.com/repos/isetbio/isetbio/issues/232/comments","events_url":"https://api.github.com/repos/isetbio/isetbio/issues/232/events","html_url":"https://github.com/isetbio/isetbio/pull/232","id":245475403,"number":232,"title":"Datamove","user":{"login":"DavidBrainard","id":1158757,"avatar_url":"https://avatars2.githubusercontent.com/u/1158757?v=4","gravatar_id":"","url":"https://api.github.com/users/DavidBrainard","html_url":"https://github.com/DavidBrainard","followers_url":"https://api.github.com/users/DavidBrainard/followers","following_url":"https://api.github.com/users/DavidBrainard/following{/other_user}","gists_url":"https://api.github.com/users/DavidBrainard/gists{/gist_id}","starred_url":"https://api.github.com/users/DavidBrainard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DavidBrainard/subscriptions","organizations_url":"https://api.github.com/users/DavidBrainard/orgs","repos_url":"https://api.github.com/users/DavidBrainard/repos","events_url":"https://api.github.com/users/DavidBrainard/events{/privacy}","received_events_url":"https://api.github.com/users/DavidBrainard/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-07-25T17:26:00Z","updated_at":"2017-07-25T17:59:57Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/isetbio/isetbio/pulls/232","html_url":"https://github.com/isetbio/isetbio/pull/232","diff_url":"https://github.com/isetbio/isetbio/pull/232.diff","patch_url":"https://github.com/isetbio/isetbio/pull/232.patch"},"body":"I did some rearranging as a start to thinking about how to document data and encapsulate and unify how we read key data.\r\n\r\na) Moved the data folder out of the isettools folder and into the top level of isetbio.  This separate the data a bit more from the code. \r\n\r\nb) Wrote isetbioDataFolder, which points to the data tree.  Changed all reads from the data folder to use this.\r\n\r\nc) Wrote ieRunAllTutorials, which runs all of the tutorials.  I did this to check that they weren't broken because of the above, and fixed a few that were. \r\n\r\nd) Step c) revealed a number of broken tutorials.  Many of these are because the switch to layers is in progress, as many of bipolar and rgc tutorials have not been updated for that and are now broken.  I moved all broken tutorials into an \"underDevelopment\" directories inside of their respective directories.  The ieRunAllTutorials script is set up to skip these (although it lists them.)\r\n\r\ne) Merged current master branch into this, and verified that validations all pass and remaining tutorials all run without error.\r\n\r\n@wandell Can you review and merge, unless something in the above is objectionable?  This change might break code outside of isetbio that finds data directly -- we were not doing that in our projects and I think almost all the data reads already go through intermediate functions so I'm not too worried.  But something to be aware of."},"comment":{"url":"https://api.github.com/repos/isetbio/isetbio/issues/comments/317819113","html_url":"https://github.com/isetbio/isetbio/pull/232#issuecomment-317819113","issue_url":"https://api.github.com/repos/isetbio/isetbio/issues/232","id":317819113,"user":{"login":"wandell","id":1837145,"avatar_url":"https://avatars1.githubusercontent.com/u/1837145?v=4","gravatar_id":"","url":"https://api.github.com/users/wandell","html_url":"https://github.com/wandell","followers_url":"https://api.github.com/users/wandell/followers","following_url":"https://api.github.com/users/wandell/following{/other_user}","gists_url":"https://api.github.com/users/wandell/gists{/gist_id}","starred_url":"https://api.github.com/users/wandell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wandell/subscriptions","organizations_url":"https://api.github.com/users/wandell/orgs","repos_url":"https://api.github.com/users/wandell/repos","events_url":"https://api.github.com/users/wandell/events{/privacy}","received_events_url":"https://api.github.com/users/wandell/received_events","type":"User","site_admin":false},"created_at":"2017-07-25T17:59:57Z","updated_at":"2017-07-25T17:59:57Z","body":"Even before checking, I can see how moving the data folder might cause a lot of problems.  There were many cases in my world when I used fullfile(isetRootPath,'data',...) to load a data set.  Maybe D65.mat or cones.mat are used for some calculation.   Perhaps you caught all of these reads from within ISET.  But what about the external scripts?\r\n"}}
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